SYLLABUS 18: Nucleotide Metabolism

Question 1

functions of purines and pyrimidines?

Answer 1

1. active precursors of DNA, RNA
2. activated intermedaites in CH (UDP) & lipid (CDP) metabolism & methylation (SAM)
3. high energy intermediates per ATP and GTP
4. metabolic regulators per cAMP and cGMP
5. part of coenzymes, NAD, FAD, CoA, B12

Question 2

difference between a nucleoside and nucleotide?

Answer 2

base + sugar = nucleoside

nucleoside + P = nucleotide

Question 3

how does purine synthesis begin?

what regulates this step?

Answer 3

with PRPP, 5-phosphoribosyl-1-pyrsophosphate

this is synthesized from ribose 5-P, which was synthesized from PPP G6P, and ATP, via PRPP synthase, aka ribose P pyrophosphokinase

reaction is feedback inhibited by IMP, AMP, GMP

Question 4

what is PRPP classification

Answer 4

an activated form of ribose 5 phosphate, as it’s created via ATP -> AMP

Question 5

what is the rate limiting step of purine biosynthesis

Answer 5

PRPP + glutamine -> 5-phosphoribosyl-1-amine catalyzed by amido phosphoribosyltransferase

glutamine becomes glutamate

this enzyme is product inhibited by IMP, AMP, GMP

Question 6

what’s the firstpurine nucleotide?

what is its structure

Answer 6

IMP, inosinate

produced by the de novo purine synthesis pathway

does not have the amino group that AMP/GMP has

Question 7

what base does IMP contain

Answer 7

hypoxanthine

Question 8

how does IMP become AMP?

Answer 8

1. inosinate uses Asp + GTP to become adenylsuccinate
2. adenylsuccinate becomes AMP, adenylate, releasing fumarate
   * GMP can inhibit step 2 in its synthesis and this drives IMP to AMP*

Question 9

how does IMP become GMP?

Answer 9

1. Inosinate becomes Xanthylate by reducing NAD+ to NADH + H+
2. Xanthylate becomes Guanylate, GMP, by using ATP -> AMP + PPi and Gln -> Glu
   * AMP can inhibit step 1 of its synthesis to drive the reaction to GMP production *

Question 10

how is there a balance between AMP and GMP synthesis

Answer 10

regulatory considerations by end product inhibition - AMP inhibits step 1 of its synthesis, and GMP inhibits step 2 of its synthesis, driving the reaction to produce the other purine

Question 11

what does this show

Answer 11

AMP and GMP regulate their own synthesis by inhibiting their own synthesis if they are in high concentration

Question 12

what happens to the AMP and GMP produced?

Answer 12

1) can degrade these purine bases as uric acid
2) can salvage these purine bases via salvage pathways

Question 13

how do interconversions btwn forms of purines / prymidines occur?

Answer 13

reversible interconversions btwn mono, di, and tri P forms of purines and pyrimidines

and XMP -> XDP via nucleoside mono P kinase

and any XDP -> XTP via nucleoside di P kinase

Question 14

what are salvage pathways

Answer 14

RNA is constantly degraded to free nitrogenous bases - i.e. adenine, guanine

if purines are degraded to free bases, they can be salvaged back to nucleotides rather than excreted

this saves energy because don’t need to synthesize more purines via energetically expensive de novo synthesis pathway

Question 15

what are the salvage enzymes

Answer 15

1. adenine phosphoribosyl transferase which catalyzes adenine -> AMP
2. hypoxanthine-guanine phosphoribosyl transferase which catalyzes hypoxanthine -> IMP and guanine -> GMP

Question 16

what causes Lesch-Nyhan syndrome?

how does it manifest?

Answer 16

absence of the salvage enzyme hypoxanthine-guanine phosphoribosyl transferase

thus cannot salvage either guanine (-> GMP) or hypoxynthine (-> IMP)

compulsive self-mutilation, mental retardation, aggressiveness, spasticity

Question 17

what happens to non-salvaged purines?

Answer 17

excreted as uric acid

Question 18

how does purine degredation -> excretion occur? describe mechanism

Answer 18

adenine -> hypoxanthine -> xanthine by xanthine oxidase

guanine -> xanthine also

xanthine is oxidized to uric acid by xanthine oxidase

uric acid is excreted into the urine

Question 19

how does xanthine oxidase work?

Answer 19

when in its oxidase form, it produces superoxide radical and H2O2 during its oxidating reactions of purine degredfation

Question 20

what chemically gout?

Answer 20

excess uric acid in the serum which forms crystalline, insoluble deposits of calcium and sodium urate in the joints

this is very painful, causes inflammation

Question 21

what is gout associated with aka what causes it but not chemically speaking?

Answer 21

1. high purine diets - eg liver
2. deficiency in salvage enzymes b/c then get excess of purines undergoing breakdown to uric acid
3. exacerbated by alcohol which increases lactic acid and competes w/ uric acid for excretion
4. kidney disease - b/c cannot excrete uric acid
5. ketoacidosis

Question 22

how can you treat gout?

Answer 22

1. decrease purine and alcohol intake in diet
2. treat with a drug like allopurinol, colchicine, or methotrexate

Question 23

how does allopurinol work?

Answer 23

gout drug treatment

it inhibits xanthine oxidase

this causes build up of hypoxanthine and xanthine, so these are excreted instead of uric acid, and these are much more soluble than uric acid

Question 24

how do the drugs colchine and methotrexate work

Answer 24

they block inflammatory reactions and the immune system which become activated in response to high levels of uric acid caused by gout

this reduces inflammation

Question 25

what is a nucleoside? nucleotide?

Answer 25

A nucleoside = base + sugar. Nucleotide = nucleoside + P

Question 26

what is hypoxathine? inosine? are these normally found in RNA or DNA?

Answer 26

Hypoxanthine is the base for IMP. Inosine is the first purine nucleotide produced via the de novo purine synthesis pathway. Hypoxanthine and Inosine are not found in RNA or DNA – they are precursors to Adenine and Guanosine which are found in RNA and DNA.

Question 27

why is folate important for purine synthesis?

Answer 27

Folate is important for purine synthesis because C2 and C8 of the purine ring come from folic acid biochemistry, the N5 N10 methenyl compound. These C thus are from serine, glycine, or histidine.

Question 28

where does ribose sugar of nucleosides come from?

Answer 28

purine synthesis starts with an activated form of ribose called 5- phosphoribosyl-1-pyrophosphate (PRPP), which is synthesized from ribose 5-P and ATP as catalyzed by PRPP synthase (or ribose P pyrophosphokinase). Recall that ribose 5-P is produced from G6P in the pentose cycle. PRPP synthase is feedback inhibited by IMP, AMP, GMP

Question 29

what regulates the conversion of IMP to either AMP or GMP?

Answer 29

The conversion of IMP to either AMP or GMP is end-product inhibited by AMP and GMP themselves; AMP inhibits its own production, and GMP inhibits its own production.

Question 30

what is basis for the lesh-nyhan syndrome?

Answer 30

Lesch-Nyhan syndrome is caused by a lack in the purine salvage enzyme hypoxanthineguanine phophoribosyl transferase, which is responsible for purine salvage of guanosine (-\> GMP) and hypoxanthine (-\> IMP).

Question 31

what are causes of gout and how is it treated

Answer 31

Gout is caused by excess uric acid in serum, which forms crystalline, insoluble deposits of calcium and sodium urate in the joints. This is very painful and causes inflammation. This is caused by several factors: high purine diet; deficiency in salvage enzymes; alcohol intake; kidney disease; and ketoacidosis. It is treated by: decreasing purine intake; decreasing alcohol intake; and treatment with a xanthine oxidase inhibitor, alluprinol or an anti-inflammatory drug such as colcihne or methotrexate.

Question 32

what is orle of xanthine oxidase in repuerfusion injury

Answer 32

ATP makes hypoxanthine when it breaks down. Hypoxanthine gets metabolized by xanthine dehydrogenase, which normally is oxidized by an NAD-dependent enzyme, X-DH, the products being NADH + Uric acid. However, in ischemic tissue, ATP isn’t being made, and there’s no oxygen. Thus lots of ATP and GTP break down to these X and HX compounds. Additionally, Xanthine-DH is converted to Xanthine Oxidase during ischemia. Xanthine Oxidase will oxidize Xanthine or Hypoxanthine, but it uses Oxygen to do so, rather than NAD in the case of the DH. This produces Uric Acid + Superoxide Radical. This causes a burst of superoxide radical, thus causing a reperfusion injury.